Sat Oct 8 16:41:02 PDT 2011 #!/bin/csh -f # input: # $1 receptor coordinates file; # $2 grid size; # $3 # of iterations for the first run; # $4 # of iterations for the second run; # $5 # of iterations for the third run; # output: # delphi map: $1.phi # log file: delphi.out set RECCRG = rec+sph2.crg set GRID = 179 set n1 = 50 set n2 = 120 set n3 = 180 set DELPHI = $DOCK_BASE/private/delphi set VDW = vdw.siz #set VDW = vdw.hydren set CRG = amb2.crg.oxt set PRM = genric.prm # three step focussing calc. if (-e ARCDAT) /bin/rm ARCDAT cp $VDW fort.11 cp $CRG fort.12 cp $RECCRG fort.13 echo "gsize=$GRID, perfil=20, bndcon=2, linit=$n1\n" >! fort.10 cat $PRM >> fort.10 time $DELPHI if ($status != 0) exit(100) echo "gsize=$GRID, perfil=60, bndcon=3, linit=$n2\n" >! fort.10 cat $PRM >> fort.10 mv fort.14 fort.18 time $DELPHI if ($status != 0) exit(100) echo "gsize=$GRID, perfil=90, bndcon=3, linit=$n3\n" >! fort.10 cat $PRM >> fort.10 mv fort.14 fort.18 time $DELPHI if ($status != 0) exit(100) /bin/rm fort.1[0-3] fort.18 ARCDAT mv fort.14 $RECCRG:r.phi ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Sat Oct 8 2011 at 16:41:02 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 245 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4525 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 0.5474229 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : dipolar x,y,z periodic bc. flags : F F F # of linear iterations : 50 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 20.00000 xmin,xmax (A): 21.28600 79.16300 ymin,ymax (A): 118.6760 183.7080 zmin,zma (A): -1.697000 59.64500 x,y,z range (A): 57.87700 65.03199 61.34200 scale (grids/A): 0.5474229 object centre (A): 50.22450 151.1920 28.97400 number of atom coordinates read : 4525 total number of charged atoms : 4394 net assigned charge : 2.000036 assigned positive charge : 697.1285 centred at (gu) : 90.61192 89.34805 87.44313 assigned negative charge : -695.1316 centred at (gu) : 90.65041 89.25100 87.47523 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 8688 nv = 96 ne = 84 npr = 90926 no. pairs analyzed = 90926 no. exposed pairs = 5639 no. arc points = 38779 no. surface atoms = 1887 nbur = 2638 mkacc time = 0.2300000 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 394 mr = 4639 m= 1 mr = 12 m= 0 mr = 0 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4800000 number of dielectric boundary points 4432 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3960 ## 529 charges are in solution ## iepsmp to db, and charging done at 0.5900000 number of grid points assigned charge 11651 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 9.1227337E-10 -1.1403487E-10 midg,1,midg; midg,igrid,midg -1.1040836E-09 9.9760644E-10 1,midg,midg; igrid,midg,midg 4.7085630E-10 -3.3775871E-10 gauss-seidel spectral radius is 0.9829085 estimated iterations to convergence 63 setup time was (sec) 0.7500000 now iterating at: 16:41:03 rms-change max change #iterations 9.1483489E-02 11.62695 at 10iterations 6.7693200E-03 0.9401360 at 20iterations 8.7479956E-04 0.1342468 at 30iterations 2.5377466E-04 3.8055420E-02 at 40iterations 8.5641252E-05 1.1604309E-02 at 50iterations finished qdiffx linear iterations at : 16:41:06 total time elapsed so far: 4.450000 # loops : 50 mean,max change (kT/e) : 8.5641252E-05 1.1604309E-02 energy calculations done at 4.450000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.620000 DelPhi exited at 16:41:07 4.626u 0.385s 0:05.27 94.8% 0+0k 0+0io 0pf+0w ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Sat Oct 8 2011 at 16:41:07 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 245 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4525 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 1.642269 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : focussing x,y,z periodic bc. flags : F F F # of linear iterations : 120 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 60.00000 xmin,xmax (A): 21.28600 79.16300 ymin,ymax (A): 118.6760 183.7080 zmin,zma (A): -1.697000 59.64500 x,y,z range (A): 57.87700 65.03199 61.34200 scale (grids/A): 1.642269 object centre (A): 50.22450 151.1920 28.97400 number of atom coordinates read : 4525 total number of charged atoms : 4394 net assigned charge : 2.000036 assigned positive charge : 697.1285 centred at (gu) : 91.83437 88.04296 82.32819 assigned negative charge : -695.1316 centred at (gu) : 91.95088 87.75262 82.42505 start vw surface at 0.1600000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 97532 reading accessible surface arcs data from file ARCDAT no. of arc points read = 38779 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 30897 mr = 67968 m= 3601 mr = 20996 m= 112 mr = 1920 m= 0 mr = 29 time to grow re-entrant surface = 0.4200000 no. cavity mid-points inaccessible to solvent = 765 time to turn everything in is 0.7900000 number of dielectric boundary points 41229 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 458 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.9300000 number of grid points assigned charge 33706 setting boundary conditions focussing boundary condition read from file fort.18 focussing potential map: qdiffxas: qdiffxs4 with an improved surfacing routine original scale (grids/A) : 0.5474229 object centre at (A) : 50.22450 151.1920 28.97400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.4811834E-03 9.6660107E-03 midg,1,midg; midg,igrid,midg 9.1282008E-03 3.4938022E-02 1,midg,midg; igrid,midg,midg -1.5259469E-02 -1.7030466E-02 gauss-seidel spectral radius is 0.9983589 estimated iterations to convergence 196 setup time was (sec) 1.120000 now iterating at: 16:41:08 rms-change max change #iterations 4.336581 160.5198 at 10iterations 1.885675 56.95761 at 20iterations 0.8164374 25.40709 at 30iterations 0.3578810 10.20562 at 40iterations 0.1558291 4.909630 at 50iterations 6.7974605E-02 1.931732 at 60iterations 2.9764228E-02 0.9424734 at 70iterations 1.2991588E-02 0.3976631 at 80iterations 5.7024150E-03 0.2036896 at 90iterations 2.5369001E-03 7.4142456E-02 at 100iterations 1.1463633E-03 3.4908295E-02 at 110iterations 5.3522695E-04 1.5932024E-02 at 120iterations finished qdiffx linear iterations at : 16:41:18 total time elapsed so far: 11.01000 # loops : 120 mean,max change (kT/e) : 5.3522695E-04 1.5932024E-02 energy calculations done at 11.01000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.18000 DelPhi exited at 16:41:19 11.187u 0.472s 0:11.92 97.7% 0+0k 0+0io 0pf+0w ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Sat Oct 8 2011 at 16:41:19 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 245 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4525 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 2.463403 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : focussing x,y,z periodic bc. flags : F F F # of linear iterations : 180 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 90.00000 xmin,xmax (A): 21.28600 79.16300 ymin,ymax (A): 118.6760 183.7080 zmin,zma (A): -1.697000 59.64500 x,y,z range (A): 57.87700 65.03199 61.34200 scale (grids/A): 2.463403 object centre (A): 50.22450 151.1920 28.97400 number of atom coordinates read : 4525 total number of charged atoms : 4394 net assigned charge : 2.000036 assigned positive charge : 697.1285 centred at (gu) : 92.75125 87.06407 78.49191 assigned negative charge : -695.1316 centred at (gu) : 92.92612 86.62878 78.63763 start vw surface at 0.1700000 fill in re-entrant regions at 0.6100000 boundary points on vw surface= 226781 reading accessible surface arcs data from file ARCDAT no. of arc points read = 38779 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 106454 mr = 166259 m= 31212 mr = 84108 m= 5794 mr = 23221 m= 522 mr = 3967 m= 10 mr = 267 m= 0 mr = 0 time to grow re-entrant surface = 1.240000 no. cavity mid-points inaccessible to solvent = 2528 time to turn everything in is 2.000000 number of dielectric boundary points 92951 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 40 iepsmp to db, and charging done at 2.140000 number of grid points assigned charge 35110 setting boundary conditions focussing boundary condition read from file fort.18 focussing potential map: qdiffxas: qdiffxs4 with an improved surfacing routine original scale (grids/A) : 1.642269 object centre at (A) : 50.22450 151.1920 28.97400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.7371037E-03 0.2063195 midg,1,midg; midg,igrid,midg 0.1437896 0.6555887 1,midg,midg; igrid,midg,midg -0.2365920 -0.2372227 gauss-seidel spectral radius is 0.9992245 estimated iterations to convergence 283 setup time was (sec) 2.340000 now iterating at: 16:41:22 rms-change max change #iterations 11.18069 345.9386 at 10iterations 6.519541 172.4154 at 20iterations 3.768162 77.75835 at 30iterations 2.175613 39.30161 at 40iterations 1.251064 22.27127 at 50iterations 0.7158180 13.85829 at 60iterations 0.4096076 7.472593 at 70iterations 0.2334125 4.522612 at 80iterations 0.1329627 2.225616 at 90iterations 7.5823143E-02 1.278577 at 100iterations 4.3085299E-02 0.8109970 at 110iterations 2.4548728E-02 0.3970718 at 120iterations 1.3965841E-02 0.2423954 at 130iterations 7.9551861E-03 0.1332023 at 140iterations 4.5393049E-03 7.4825525E-02 at 150iterations 2.5906956E-03 4.5257568E-02 at 160iterations 1.4888842E-03 2.5625557E-02 at 170iterations 8.6115394E-04 1.4996052E-02 at 180iterations finished qdiffx linear iterations at : 16:41:39 total time elapsed so far: 19.17000 # loops : 180 mean,max change (kT/e) : 8.6115394E-04 1.4996052E-02 energy calculations done at 19.17000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 19.33000 DelPhi exited at 16:41:39 19.338u 0.496s 0:20.09 98.6% 0+0k 0+0io 0pf+0w